I have had wood floors since I got both Rex and Rowdy. Rowdy is not neutered so he will always mark. He has marked the wood floors plenty of times with absolutely no issues - however, my wood floors have LOTS of wood grain and differing colors. I don't think there have been any spots, but I can't be absolutely sure. There has been no warping of any kind. Rowdy doesn't pee a bit pool though, he just sprinkles a few marks. Both he and Rex are trained to go outside and they don't have to stay in a pen, there is always someone here at the house and if we are all gone at the same time (a rarity) then I keep them in the den which has a stained concrete floor - this floor is a GODSEND when training puppies - all my pups are confinded to the big den with the concrete floor until they are at least 75% trained. I will have to say that Rex is neutered and so when he "goes" it is a big pool (well big for a 6 lb Yorkie
) and as such, if he were peeing on the wood floor - which he never does, he never goes in the house - then it might be more of an issue.
Good luck with your decision. If you keep this bumped to the top, you will get lots of responses - many of us have ripped out our carpet and put down wood, laminate or tile.